Index: /issm/trunk-jpl/etc/environment.sh
===================================================================
--- /issm/trunk-jpl/etc/environment.sh	(revision 13148)
+++ /issm/trunk-jpl/etc/environment.sh	(revision 13149)
@@ -1,3 +1,46 @@
 #ISSM_DIR and ISSM_ARCH should have been defined already in your shell settings file (.bashrc, .cshrc, etc ...)
+
+pathprepend(){ #{{{
+	if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
+		PATH="$1:$PATH"
+	fi
+} #}}}
+pathappend(){ #{{{
+	if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then
+		export PATH="$PATH:$1"
+	fi
+} #}}}
+libpathprepend(){ #{{{
+	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export LD_LIBRARY_PATH="$1:$LD_LIBRARY_PATH"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$1:$LD_RUN_PATH"
+	fi
+} #}}}
+libpathappend(){ #{{{
+	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$LD_RUN_PATH:$1"
+	fi
+} #}}}
+dylibpathprepend(){ #{{{
+	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export LD_LIBRARY_PATH="$1:$LD_LIBRARY_PATH"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$1:$LD_RUN_PATH"
+	fi
+} #}}}
+dylibpathappend(){ #{{{
+	if [ -d "$1" ] && [[ ":$LD_LIBRARY_PATH:" != *":$1:"* ]]; then
+		export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1"
+	fi
+	if [ -d "$1" ] && [[ ":$LD_RUN_PATH:" != *":$1:"* ]]; then
+		export LD_RUN_PATH="$LD_RUN_PATH:$1"
+	fi
+} #}}}
 
 #FIXME: during installation packages are installed one by one but environment.sh was sourced
@@ -12,122 +55,66 @@
 
 #Some basic path, in case it is not included by default
-export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib"
-export LD_RUN_PATH="$LD_RUN_PATH:/usr/local/lib"
+libpathappend "/usr/local/lib"
 
 #Load ISSM scripts
-export PATH="$PATH:$ISSM_DIR/scripts"
-
-#MATLAB
+pathappend "$ISSM_DIR/scripts"
+
 MATLAB_DIR="$ISSM_DIR/externalpackages/matlab/install"
-#if [ -d "$MATLAB_DIR" ]; then
-	export MATLAB_DIR
-	export PATH="$MATLAB_DIR/bin:$PATH" #take precedence over /usr/local/bin/matlab
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MATLAB_DIR/lib"
-	export LD_RUN_PATH="$LD_RUN_PATH:$MATLAB_DIR/lib"
-#fi
-
-#MPI
+export MATLAB_DIR
+pathprepend   "$MATLAB_DIR/bin" #take precedence over /usr/local/bin/matlab
+libpathappend "$MATLAB_DIR/lib"
+
 MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install"
-#if [ -d "$MPI_DIR" ]; then
-	export MPI_DIR
-	export PATH="$MPI_DIR/bin:$PATH"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$MPI_DIR/lib"
-	export LD_RUN_PATH="$LD_RUN_PATH:$MPI_DIR/lib"
-	export MANPATH="$MANPATH:$MPI_DIR/man"
-#fi
-
-#PETSC
+export MPI_DIR
+pathprepend   "$MPI_DIR/bin"
+libpathappend "$MPI_DIR/lib"
+
 PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install"
-#if [ -d "$PETSC_DIR" ]; then
-	export PETSC_DIR
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PETSC_DIR/lib:$PETSC_DIR/lib"
-	export LD_RUN_PATH="$LD_RUN_PATH:$PETSC_DIR/lib"
-#fi
-
-#SLEPC
+export PETSC_DIR
+libpathappend "$PETSC_DIR/lib"
+
 SLEPC_DIR="$ISSM_DIR/externalpackages/slepc/install"
-if [ -d "$SLEPC_DIR" ]; then
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SLEPC_DIR/lib/$ISSM_ARCH"
-	export LD_RUN_PATH="$LD_RUN_PATH:$SLEPC_DIR/lib/$ISSM_ARCH"
-fi
-
-#PETSC
+libpathappend "$SLEPC_DIR/lib/$ISSM_ARCH"
+
 TAO_DIR="$ISSM_DIR/externalpackages/tao/install"
-if [ -d "$TAO_DIR" ]; then
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$TAO_DIR/lib:$TAO_DIR/lib"
-	export LD_RUN_PATH="$LD_RUN_PATH:$TAO_DIR/lib"
-fi
-
-#Dakota
+libpathappend "$TAO_DIR/lib"
+
 DAKOTA_DIR="$ISSM_DIR/externalpackages/dakota/install"
-if [ -d "$DAKOTA_DIR" ]; then
-	export PATH="$PATH:$DAKOTA_DIR/bin"
-	export MANPATH="$MANPATH:$MPI_DIR/man:$DAKOTA_DIR/docs/man:$DAKOTA_DIR/docs/man-ref"
-fi
-
-#Doxygen
+pathappend "$DAKOTA_DIR/bin"
+
 DOXYGEN_DIR="$ISSM_DIR/externalpackages/doxygen/install"
-if [ -d "$DOXYGEN_DIR" ]; then
-	export MANPATH="$MANPATH:$DOXYGEN_DIR/man"
-	export PATH="$PATH:$DOXYGEN_DIR/bin"
-fi
-
-#AUTOCONF
+pathappend "$DOXYGEN_DIR/bin"
+
 AUTOCONF_DIR="$ISSM_DIR/externalpackages/autoconf/install"
-#if [ -d "$AUTOCONF_DIR" ]; then
-	export PATH="$AUTOCONF_DIR/bin:$PATH"
-#fi
-
-#AUTOMAKE
+pathprepend "$AUTOCONF_DIR/bin"
+
 AUTOMAKE_DIR="$ISSM_DIR/externalpackages/automake/install"
-#if [ -d "$AUTOMAKE_DIR" ]; then
-	export PATH="$AUTOMAKE_DIR/bin:$PATH"
-#fi
-
-#LIBTOOL
+pathprepend "$AUTOMAKE_DIR/bin"
+
 LIBTOOL_DIR="$ISSM_DIR/externalpackages/libtool/install"
-#if [ -d "$LIBTOOL_DIR" ]; then
-	export PATH="$LIBTOOL_DIR/bin:$PATH"
-#fi
-
-#SDK
+pathprepend "$LIBTOOL_DIR/bin"
+
 SDK_DIR="C:/MicrosoftVisualStudio 9.0/Microsoft Visual C++ 2008 Express Edition with SP1 - ENU"
-if [ -d "$SDK_DIR" ]; then
-	export PATH="$PATH:$SDK_DIR"
-fi
-
-#SSH
+pathappend "$SDK_DIR"
+
 SSH_DIR="$ISSM_DIR/externalpackages/ssh"
-if [ -d "$SSH_DIR" ]; then
-	export PATH="$PATH:$SSH_DIR"
-fi
-
-#VALGRIND
+pathappend "$SSH_DIR"
+
 VALGRIND_DIR="$ISSM_DIR/externalpackages/valgrind/install"
-if [ -d "$VALGRIND_DIR" ]; then
-	export PATH="$VALGRIND_DIR/bin:$PATH"
-fi
-
-#CPPCHECK
+pathprepend "$VALGRIND_DIR/bin"
+
 CPPCHECK_DIR="$ISSM_DIR/externalpackages/cppcheck/install"
-if [ -d "$CPPCHECK_DIR" ]; then
-	export PATH="$PATH:$CPPCHECK_DIR/bin"
-fi
-
-#GDAL
+pathappend "$CPPCHECK_DIR/bin"
+
 GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install"
-if [ -d "$GDAL_DIR" ]; then
-	export PATH="$GDAL_DIR/bin:$PATH"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GDAL_DIR/lib"
-fi
-
-#MERCURIAL
+pathprepend "$GDAL_DIR/bin:$PATH"
+libpathappend "$GDAL_DIR/lib"
+
 MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install"
 if [ -d "$MERCURIAL_DIR" ]; then
 	export PYTHONPATH="$PYTHONPATH:$MERCURIAL_DIR/mercurial/pure/"
-	export PATH="$PATH:$MERCURIAL_DIR/"
-fi
-
-#BOOST
+	pathappend "$MERCURIAL_DIR"
+fi
+
 BOOST_DIR="$ISSM_DIR/externalpackages/boost/install"
 BOOSTROOT="$ISSM_DIR/externalpackages/boost/install"
@@ -135,10 +122,9 @@
 	export BOOSTROOT
 	export BOOST_DIR
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$BOOST_DIR/lib"
-	export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$BOOST_DIR/lib"
-	export PATH="$PATH:$BOOST_DIR/bin"
-fi
-
-#XERCES
+	libpathappend   "$BOOST_DIR/lib"
+	dylibpathappend "$BOOST_DIR/lib"
+	pathappend      "$BOOST_DIR/bin"
+fi
+
 XERCESROOT="$ISSM_DIR/externalpackages/xerces/install"
 XERCESCROOT="$ISSM_DIR/externalpackages/xerces/src"
@@ -148,5 +134,4 @@
 fi
 
-#xaifBooster
 XAIF_DIR="$ISSM_DIR/externalpackages/xaifbooster/xaifBooster"
 XAIFBOOSTERROOT="$ISSM_DIR/externalpackages/xaifbooster/"
@@ -160,5 +145,4 @@
 fi
 
-#angel
 ANGELROOT="$ISSM_DIR/externalpackages/angel/angel"
 if [ -d "$ANGELROOT" ]; then
@@ -166,203 +150,111 @@
 fi
 
-#openanalysis
 OPENANALYSISROOT="$ISSM_DIR/externalpackages/openanalysis/install"
 if [ -d "$OPENANALYSISROOT" ]; then
 	export OPENANALYSISROOT
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$OPENANALYSISROOT/lib"
-fi
-
-#JAVA
+	libpathappend "$OPENANALYSISROOT/lib"
+fi
+
 JVM_DIR="/usr/local/gcc/4.3.2/lib64/gcj-4.3.2-9/"
-if [ -d "$JVM_DIR" ]; then
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$JVM_DIR"
-fi
-
-#BBFTP
+libpathappend "$JVM_DIR"
+
 BBFTP_DIR="$ISSM_DIR/externalpackages/bbftp/install"
-if [ -d "$BBFTP_DIR" ]; then
-	export PATH="$PATH:$BBFTP_DIR/bin"
-fi
-
-#ADIC
+pathappend "$BBFTP_DIR/bin"
+
 ADIC_DIR="$ISSM_DIR/externalpackages/adic/install"
-if [ -d "$ADIC_DIR" ]; then
-	export PATH="$PATH:$ADIC_DIR/bin"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$ADIC_DIR/lib"
-	export LD_RUN_PATH="$LD_RUN_PATH:$ADIC_DIR/lib"
-fi
-
-#COLPACK
+pathappend "$ADIC_DIR/bin"
+libpathappend "$ADIC_DIR/lib"
+
 COLPACK_DIR="$ISSM_DIR/externalpackages/colpack/install"
-if [ -d "$COLPACK_DIR" ]; then
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$COLPACK_DIR/lib"
-	export LD_RUN_PATH="$LD_RUN_PATH:$COLPACK_DIR/lib"
-fi
-
-#ECLIPSE
+libpathappend "$COLPACK_DIR/lib"
+
 ECLIPSE_DIR="$ISSM_DIR/externalpackages/eclipse/install"
-if [ -d "$ECLIPSE_DIR" ]; then
-	export PATH="$PATH:$ECLIPSE_DIR"
-fi
-
-#APPSCAN
+pathappend "$ECLIPSE_DIR"
+
 APPSCAN_DIR="$ISSM_DIR/externalpackages/appscan/install"
-if [ -d "$APPSCAN_DIR" ]; then
-	export PATH="$PATH:$APPSCAN_DIR/bin"
-fi
-
-#RATS
+pathappend "$APPSCAN_DIR/bin"
+
 RATS_DIR="$ISSM_DIR/externalpackages/rats/install"
-if [ -d "$RATS_DIR" ]; then
-	export PATH="$PATH:$RATS_DIR/bin"
-fi
-
-#DYSON
+pathappend "$RATS_DIR/bin"
+
 DYSON_DIR="$ISSM_DIR/externalpackages/dyson/"
-if [ -d "$DYSON_DIR" ]; then
-	export PATH="$PATH:$DYSON_DIR"
-fi
-
-#CMAKE
+pathappend "$DYSON_DIR"
+
 CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install"
-if [ -d "$CMAKE_DIR" ]; then
-	export PATH="$PATH:$CMAKE_DIR/bin"
-fi
-
-#SHAPELIB
+pathappend "$CMAKE_DIR/bin"
+
 SHAPELIB_DIR="$ISSM_DIR/externalpackages/shapelib/install"
-if [ -d "$SHAPELIB_DIR" ]; then
-	export PATH="$PATH:$SHAPELIB_DIR/exec"
-fi
-
-#CCCL
+pathappend "$SHAPELIB_DIR/exec"
+
 CCCL_DIR="$ISSM_DIR/externalpackages/cccl/install"
-if [ -d "$CCCL_DIR" ]; then
-	export PATH="$PATH:$CCCL_DIR/bin"
-fi
-
-#PACKAGEMAKER
+pathappend "$CCCL_DIR/bin"
+
 PACKAGEMAKER_DIR="$ISSM_DIR/externalpackages/packagemaker/install"
-if [ -d "$PACKAGEMAKER_DIR" ]; then
-	export PATH="$PATH:$PACKAGEMAKER_DIR"
-fi
-
-#ANDROID_NDK:
+pathappend "$PACKAGEMAKER_DIR"
+
 ANDROID_NDK_DIR="$ISSM_DIR/externalpackages/android-ndk/install"
-if [ -d "$ANDROID_NDK_DIR" ]; then
-	export PATH="$PATH:$ANDROID_NDK_DIR/"
-fi
-
-#ANDROID_SDK
+pathappend "$ANDROID_NDK_DIR/"
+
 ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install-sdk"
-if [ -d "$ANDROID_SDK_DIR" ]; then
-	export PATH="$PATH:$ANDROID_SDK_DIR/"
-fi
-
-#GSL
+pathappend "$ANDROID_SDK_DIR/"
+
 GSL_DIR="$ISSM_DIR/externalpackages/gsl/install"
-if [ -d "$GSL_DIR" ]; then
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GSL_DIR/lib"
-	export LD_RUN_PATH="$LD_RUN_PATH:$GSL_DIR/lib"
-fi
-
-#GMAKE
+libpathappend "$GSL_DIR/lib"
+
 GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install"
-if [ -d "$GMAKE_DIR" ]; then
-	export PATH="$GMAKE_DIR/bin:$PATH"
-fi
-
-#PYTHON
+pathprepend "$GMAKE_DIR/bin"
+
 PYTHON_DIR="$ISSM_DIR/externalpackages/python/install"
 if [ -d "$PYTHON_DIR" ]; then
-	PYTHONSTARTUP="$ISSM_DIR/startup.py"
-	export PATH="$PYTHON_DIR/bin:$PATH"
 	export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/src/modules/python"
-	export LD_LIBRARY_PATH=$ISSM_DIR/src/modules/python:$ISSM_DIR/externalpackages/python/install/lib:$LD_LIBRARY_PATH
 	export PYTHONSTARTUP="$ISSM_DIR/startup.py"
-fi
-
-#MODELE
+	pathprepend    "$PYTHON_DIR/bin"
+	libpathprepend "$ISSM_DIR/src/modules/python"
+	libpathprepend "$PYTHON_DIR/lib"
+fi
+
 MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install"
-if [ -d "$MODELE_DIR" ]; then
-	export PATH="$MODELE_DIR/src/exec:$PATH"
-fi
-
-#GIT
+pathappend "$MODELE_DIR/src/exec"
+
 GIT_DIR="$ISSM_DIR/externalpackages/git/install"
-if [ -d "$GIT_DIR" ]; then
-	export PATH="$PATH:$GIT_DIR/bin"
-fi
-
-#NCVIEW
+pathappend "$GIT_DIR/bin"
+
 NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install"
-if [ -d "$NCVIEW_DIR" ]; then
-	export PATH="$PATH:$NCVIEW_DIR"
-fi
-
-#TCLX
+pathappend "$NCVIEW_DIR"
+
 TCLX_DIR="$ISSM_DIR/externalpackages/tclx/install/lib/tclx8.4"
-if [ -d "$TCLX_DIR" ]; then
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$TCLX_DIR"
-	export LD_RUN_PATH="$LD_RUN_PATH:$TCLX_DIR"
-fi
-
-#ASPELL
+libpathappend "$TCLX_DIR"
+
 ASPELL_DIR="$ISSM_DIR/externalpackages/aspell/install"
-if [ -d "$ASPELL_DIR" ]; then
-	export PATH="$ASPELL_DIR/bin:$PATH"
-fi
-
-#ESMF
-ESMF_DIR="$ISSM_DIR/externalpackages/esmf/esmf"
-if [ -d "$ESMF_DIR" ]; then
-	export ESMF_COMPILER=gfortran
-	export ESMF_COMM=mpich2
-fi
-
-#HDF5
+pathappend "$ASPELL_DIR/bin:$PATH"
+
 HDF5_DIR="$ISSM_DIR/externalpackages/hdf5/install"
 if [ -d "$HDF5_DIR" ]; then
-	export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HDF5_DIR/lib"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HDF5_DIR/lib"
+	dylibpathappend "$HDF5_DIR/lib"
+	libpathappend "$HDF5_DIR/lib"
 	export LIBRARY_PATH="$LIBRARY_PATH:$HDF5_DIR/lib"
 	export C_INCLUDE_PATH="$C_INCLUDE_PATH:$HDF5_DIR/include"
 fi
 
-#SVN
 SVN_DIR="$ISSM_DIR/externalpackages/svn/install"
 if [ -d "$SVN_DIR" ]; then
-	export PATH="$SVN_DIR/bin:$PATH"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SVN_DIR/lib"
-	export LIBRARY_PATH="$LIBRARY_PATH:$SVN_DIR/lib"
-fi
-
-#APR
+	pathprepend   "$SVN_DIR/bin"
+	libpathappend "$SVN_DIR/lib"
+fi
+
 APR_DIR="$ISSM_DIR/externalpackages/apr/install"
 if [ -d "$APR_DIR" ]; then
-	export PATH="$APR_DIR/bin:$PATH"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$APR_DIR/lib"
-	export LIBRARY_PATH="$LIBRARY_PATH:$APR_DIR/lib"
-fi
-
-#APR_UTIL
+	pathappend    "$APR_DIR/bin"
+	libpathappend "$APR_DIR/lib"
+fi
+
 APR_UTIL_DIR="$ISSM_DIR/externalpackages/apr-util/install"
-if [ -d "$APR_UTIL_DIR" ]; then
-	export PATH="$APR_UTIL_DIR/bin:$PATH"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$APR_UTIL_DIR/lib"
-	export LIBRARY_PATH="$LIBRARY_PATH:$APR_UTIL_DIR/lib"
-fi
-
-#SQLITE
+pathappend   "$APR_UTIL_DIR/bin:$PATH"
+libpathappend "$APR_UTIL_DIR/lib"
+
 SQLITE_DIR="$ISSM_DIR/externalpackages/sqlite/install"
-if [ -d "$SQLITE_DIR" ]; then
-	export PATH="$SQLITE_DIR/bin:$PATH"
-	export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$SQLITE_DIR/lib"
-	export LIBRARY_PATH="$LIBRARY_PATH:$SQLITE_DIR/lib"
-fi
-
-#YAMS
+pathappend   "$SQLITE_DIR/bin"
+libpathappend "$SQLITE_DIR/lib"
+
 YAMS_DIR="$ISSM_DIR/externalpackages/yams/install"
-if [ -d "$YAMS_DIR" ]; then
-	export PATH="$PATH:$YAMS_DIR"
-fi
+pathappend   "$YAMS_DIR"